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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
 
                             WASHINGTON, D.C. 20549
 
                            ------------------------
 
                                 FORM 10-Q/A-1
 
  /X/    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
         SECURITIES EXCHANGE ACT OF 1934
 
               FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 1998
                                       OR
 
  / /    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
         SECURITIES EXCHANGE ACT OF 1934
 
        FOR THE TRANSITION PERIOD FROM ______________ TO ______________
 
                         COMMISSION FILE NUMBER 0-27628
 
                            ------------------------
 
                                 SUPERGEN, INC.
 
             (Exact name of registrant as specified in its charter)
 
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<S>                                             <C>
                   DELAWARE                                       91-1841574
         (State or other jurisdiction                           (IRS Employer
      of incorporation or organization)                     Identification Number)
 
   TWO ANNABEL LANE, SUITE 220, SAN RAMON,                          94583
                  CALIFORNIA                                      (Zip code)
   (Address of principal executive offices)
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                                 (925) 327-0200
              (Registrant's telephone number, including area code)
 
                                 NOT APPLICABLE
   (Former name, former address and former fiscal year, if changed since last
                                    report)
 
                            ------------------------
 
    Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports) and (2) has been subject to such
filing requirements for the past 90 days. Yes /X/  No / /
 
                      APPLICABLE ONLY TO CORPORATE ISSUERS
 
    The number of shares of the registrant's Common Stock, $.001 par value,
outstanding as of October 30, 1998, was 20,381,439.
 
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ITEM 2.
 
                    MANAGEMENT'S DISCUSSION AND ANALYSIS OF
                 FINANCIAL CONDITION AND RESULTS OF OPERATIONS
 
    PRELIMINARY NOTE REGARDING FORWARD-LOOKING STATEMENTS
 
    THIS QUARTERLY REPORT ON FORM 10-Q CONTAINS FORWARD-LOOKING STATEMENTS
WITHIN THE MEANING OF SECTION 27A OF THE SECURITIES ACT OF 1933 AND SECTION 21E
OF THE SECURITIES EXCHANGE ACT OF 1934. THESE FORWARD-LOOKING STATEMENTS
REPRESENT THE COMPANY'S EXPECTATIONS OR BELIEFS CONCERNING FUTURE EVENTS AND
INCLUDE STATEMENTS, AMONG OTHERS, REGARDING:
 
    - THE TIMING AND PROGRESS OF THE DEVELOPMENT OF THE COMPANY'S PROPOSED
      PRODUCTS,
 
    - FILING FOR AND RECEIVING REGULATORY APPROVALS,
 
    - ACQUIRING ADDITIONAL PRODUCTS AND TECHNOLOGIES,
 
    - ANTICIPATING THE MARKET OPPORTUNITIES FOR ITS EXTRA AND PROPRIETARY
      PRODUCTS,
 
    - MARKETING CURRENT AND PROPOSED PRODUCTS TO HOSPITAL BUYING GROUPS AND
      OTHERS,
 
    - DEVELOPING PARTNERSHIP RELATIONSHIPS,
 
    - INCURRING OPERATING EXPENSES AND LOSSES AND REQUIRING ADDITIONAL CAPITAL,
      AND
 
    - INCURRING CAPITAL EXPENDITURES.
 
    ACTUAL RESULTS COULD DIFFER MATERIALLY FROM THOSE PROJECTED IN THE
FORWARD-LOOKING STATEMENTS AS A RESULT OF A VARIETY OF FACTORS, INCLUDING THOSE
SET FORTH UNDER "--FACTORS AFFECTING FUTURE OPERATING RESULTS" BELOW AND
ELSEWHERE IN THIS REPORT.
 
OVERVIEW
 
    SuperGen, Inc. ("SuperGen" or the "Company") is an emerging pharmaceutical
company dedicated to the acquisition, rapid development and commercialization of
products for the treatment of life-threatening diseases, particularly cancer. A
key element of the Company's strategy is to identify, acquire and develop
pharmaceutical products in the later stages of development. The Company believes
this strategy will shorten the research and development cycle and thereby
minimize the time, expense and technical risk associated with drug development.
The Company's primary oncology programs target leukemias and lymphomas, solid
tumors and the development of the Company's proprietary Extra technology (its
enhanced line of already established anticancer drugs). SuperGen also seeks to
expand its portfolio of anticancer drugs through the acquisition of products and
product candidates that complement its portfolio and provide the Company with
market opportunities. The Company also has non-oncology programs in the large
market areas of anemias and other blood cell disorders, obesity/diabetes and
certain autoimmune diseases. The Company intends to seek partnership
opportunities in these areas.
 
    Since late 1996, the Company has actively marketed several pharmaceutical
products. The Company acquired the proprietary drug Nipent-Registered Trademark-
(pentostatin for injection), along with associated North American marketing
rights, in 1996. In December 1997, the Company received governmental approval to
sell Nipent-Registered Trademark- manufactured under its own Supplemental New
Drug Application. Nipent-Registered Trademark- is indicated for the treatment of
Hairy Cell Leukemia and it has Orphan Drug Designation for both chronic
lymphocytic leukemia and cutaneous T-cell lymphoma. In April 1998, the Company
received FDA approval to market the generic drug mitomycin for injection.
Mitomycin, originally developed and marketed by Bristol-Meyers Squibb under the
tradename Mutamycin-Registered Trademark-, is approved in the U.S. for the
treatment of adenocarcinoma of the stomach and pancreas in combination with
other approved chemotherapeutics. The Company began to sell mitomycin in June
1998.
 
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    Sales of Nipent-Registered Trademark- were responsible for 96% of product
revenues in the first nine months of 1998 and 81% of product revenues for the
same period in 1997. Remaining product revenues in 1998 consisted of sales of
mitomycin, and remaining product revenues in 1997 consisted of sales of several
generic products purchased in 1997 and 1996.
 
    In September 1997, the Company acquired exclusive worldwide rights to a
patented anticancer compound (RFS2000), which is currently in Phase III human
trials for pancreatic cancer, the fifth leading cause of cancer death. It has
also shown activity against an array of solid tumors in animal and initial human
studies with a favorable side effect profile. At the end of 1997, SuperGen filed
for governmental approval for its first Extra product, Mito Extra. The Food and
Drug Administration accepted that filing for review in February 1998. The
Company intends to file for approval of several additional Extra and generic
anticancer products over the next several years. Also, the Company has continued
development of a proprietary blood cell disorder product for the treatment of
aplastic anemia (and other anemias associated with chemotherapy, radiotherapy,
and renal failure). SuperGen's proprietary obesity/diabetes pill, which has
shown promise in early preclinical and human studies, is currently in Phase II
clinical trials for a genetic disorder leading to chronic obesity and is
expanding into multi-center Phase I/II trials for Type II diabetes. The Company
has received Orphan Drug Designations for its aplastic anemia agent and obesity
pill for the treatment of a genetic disorder leading to chronic obesity.
 
    The Company has incurred losses in each year since its inception and has
accumulated approximately $51.5 million in net losses through September 30,
1998. Revenue from future product sales or other sources may never be sufficient
to fund operations and the Company may never achieve profitability or positive
cash flow.
 
    The Company expects its research and development expenses to increase as a
result of expanded clinical trials of RFS 2000, Nipent-Registered Trademark-,
the Extra product line and other drugs. The Company expects its marketing and
sales expenses to increase as it expands its United States direct sales and
marketing organization.
 
    The Company's future quarterly operating results will depend on a variety of
factors, including
 
    - changes in the Company's level of research and development, including the
      timing of any expansion of clinical trials,
 
    - acquisitions of products or technology,
 
    - regulatory approvals of new products or expanded labeling of existing
      products,
 
    - the price, volume and timing of sales of the Company's products,
 
    - the Company's ability to successfully manufacture approved products for
      sale,
 
    - the mix between Nipent-Registered Trademark- sales in the United States
      and those under a supply agreement for sale outside North America, and
 
    - variations in gross margins of the Company's products, which may be
      affected by the sales mix referred to above, competitive pricing
      pressures, and fluctuations in manufacturing yields.
 
    In addition, sales of any product in any given period may include a
significant amount of orders for inventory by distributors and wholesalers and
may not be indicative of actual demand for products by physicians and patients.
There can be no assurance that distributors or wholesalers will be able to
forecast demand for product accurately. The Company expects quarterly operating
results to fluctuate in the future.
 
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RESULTS OF OPERATIONS
 
    THREE MONTHS ENDED SEPTEMBER 30, 1998 COMPARED TO THREE MONTHS ENDED
     SEPTEMBER 30, 1997.
 
    Total revenues were $537,000 compared to $302,000 in 1997. Revenues in both
periods consisted entirely of product sales. The increase in revenues in 1998
was due primarily to higher sales volumes of Nipent-Registered Trademark-, which
resulted from sales of Nipent-Registered Trademark- under a supply agreement for
sale outside North America, which commenced in March 1998. Sales of mitomycin,
which commenced in June 1998, also contributed to the increased revenues in
1998.
 
    Gross margin on sales of Nipent-Registered Trademark- was negative in both
1998 and 1997. In 1998, margins on sales of Nipent-Registered Trademark- were
adversely affected by a $253,000 charge to cost of sales for manufacturing
capacity costs and lower unit selling prices for Nipent-Registered Trademark-
sold under the supply agreement (relative to selling prices for direct sales of
Nipent-Registered Trademark- in the United States). Margins in 1997 were
adversely affected by low selling prices for certain generic products and high
unit cost for Nipent-Registered Trademark- inventory. In 1997, sales of
Nipent-Registered Trademark- consisted entirely of inventory acquired from
Warner-Lambert Company and margins were affected by the relatively high unit
cost of that inventory. The unit cost of manufactured
Nipent-Registered Trademark- has been, and is expected to continue to be,
significantly lower than the unit cost assigned to the
Nipent-Registered Trademark- inventory acquired from Warner-Lambert Company.
However, the Company is in the early stages of Nipent-Registered Trademark-
sales and manufacturing and current margins may not be indicative of future
margins due to possible variations in average selling prices and manufacturing
costs.
 
    Research and development expenses were $2,592,000 in 1998 compared to
$2,275,000 in 1997. The increased expense was primarily due to manufacturing and
clinical costs associated with RFS2000, and expansion of the research and
development staff. These increased costs were partially offset by the effect of
Nipent-Registered Trademark- manufacturing start-up costs incurred in 1997 and
not duplicated in 1998.
 
    Sales and marketing expenses were $738,000 in 1998 compared to $441,000 in
1997. The increased expense was primarily due to advertising and related costs
to support Nipent-Registered Trademark- sales in 1998. Also, the Company has
expanded its sales and professional services staff resulting in additional
expense in 1998.
 
    General and Administrative expenses were $947,000 in 1998 compared to
$912,000 in 1997. The increased expense in 1998 included costs, totaling
$120,000, related to the termination of a consultancy relationship with a former
director and costs resulting from a slight increase in administrative staff.
These increased expenses were offset by lower legal and other costs in 1998.
Such costs incurred in 1997 related to technology acquisition and equity
financing transactions, and were not repeated in 1998.
 
    In 1997, the Company incurred a charge of $1,875,000 for the acquisition of
in-process research and development, relating to the acquisition of RFS2000.
 
    NINE MONTHS ENDED SEPTEMBER 30, 1998 COMPARED TO NINE MONTHS ENDED SEPTEMBER
     30, 1997.
 
    Total revenues were $2,089,000 in 1998 compared to $1,282,000 in 1997. The
increase in revenues was due primarily to higher sales volumes of
Nipent-Registered Trademark- in 1998, which resulted principally from sales of
Nipent-Registered Trademark- under a supply agreement for sale outside North
America, which commenced in March 1998. The Company began to sell mitomycin late
in the second quarter of 1998 and revenues from sales of mitomycin contributed
slightly to the overall revenue increase.
 
    Gross margin was higher in 1998 due primarily to the lower unit cost of
Nipent-Registered Trademark- sold. This positive effect upon margin was
partially offset by lower selling prices for Nipent-Registered Trademark- sold
under the supply agreement and a $253,000 charge to cost of sales for
manufacturing capacity costs. The Company is in the early stages of
Nipent-Registered Trademark- sales and manufacturing and current margins may not
be indicative of future margins due to possible variations in average selling
prices and manufacturing costs.
 
    Research and development expenses were $7,630,000 in 1998 compared to
$5,903,000 in 1997. Product formulation and development costs associated with
RFS 2000, Nipent-Registered Trademark- and mitomycin contributed to the
 
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overall increase in expenses in 1998. Costs attributable to expansion of the
research and development staff also contributed to the increase in expense, as
did the Company's investment of $200,000 in a related party in the first quarter
of 1998.
 
    Sales and marketing expenses were $2,185,000 in 1998 compared to $1,231,000
in 1997. This increase was primarily due to costs reflecting the expansion of
the sales and marketing group from six at December 31, 1996 to 15 at September
30, 1998. In 1998 the Company initiated media advertising for
Nipent-Registered Trademark- and increased its presence at strategic trade
shows. Costs associated with these activities also contributed to the overall
increase in expenses.
 
    General and Administrative expenses were $2,885,000 in 1998, compared to
$2,173,000 in 1997. The increase was due principally to consultancy and other
costs relating to investor relations, patent related legal fees and enhancements
in information technology. Higher facilities and personnel costs also
contributed to the overall increase in expense. The Company moved into larger
administrative offices in March of 1997 and the administrative staff has grown
slightly to accommodate increases in headcount and business activities.
 
    In 1997, the Company incurred the following charges for the acquisition of
in-process research and development:
 
    - $831,000 related to the acquisition of the generic anticancer drug
      etoposide, and
 
    - $1,875,000 for the acquisition of RFS2000.
 
LIQUIDITY AND CAPITAL RESOURCES
 
    The Company's cash, cash equivalents and marketable securities totaled $12.7
million at September 30, 1998 compared to $23.3 million at December 31, 1997.
The net cash used in operating activities of $10.3 million in the first nine
months of 1998 reflected the net loss of $11.2 million partially offset by non-
cash charges for depreciation, stock options granted to consultants and the
termination of a consultancy relationship with a former director. Cash used for
purchases of property and equipment was $608,000, principally for equipment,
fixtures and computer equipment at the Company's research facility established
in Pleasanton, California late in 1997.
 
    The Company believes that its cash, cash equivalents and investments in
marketable securities on-hand at September 30, 1998 will satisfy its budgeted
cash requirements for approximately 12 months, based on the Company's current
operating plan. The primary planned uses of cash during that period are:
 
    - funding operations,
 
    - conducting clinical testing of potential proprietary and Extra-TM-
      products,
 
    - marketing for expanded indications for Nipent-Registered Trademark- that
      may be developed, and
 
    - continuing research and development programs.
 
    The Company is actively considering future contractual arrangements that
would require significant financial commitments, particularly for acquiring
rights to additional drug candidates and for clinical trials for existing and
new drug candidates. The Company will need to raise capital before the third
quarter of 1999 if cash needs exceed budgeted amounts. The Company does not
anticipate significant capital expenditures for the remainder of 1998.
 
    The Company may seek such additional funding through public or private
financings or collaborative or other arrangements with third parties. The
Company has no credit facility or other committed sources of capital. There can
be no assurance that additional funds will be available on acceptable terms, if
at all. See "--Factors Affecting Future Operating Results."
 
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FACTORS AFFECTING FUTURE OPERATING RESULTS
 
    As the future operating results of the Company cannot be accurately
predicted, the following factors should be carefully reviewed together with the
other information contained in this quarterly report on Form 10-Q.
 
    - HISTORY OF OPERATING LOSSES. The Company has incurred losses in every
      fiscal period to date and expects to continue to incur significant
      operating losses. The likelihood of the long-term success of the Company
      must be considered in light of the expenses, difficulties and delays
      frequently encountered in the development, commercialization and
      manufacturing of new pharmaceutical products, as well as competition and
      the burdensome regulatory environment in which the Company operates. The
      Company has limited experience in each of these areas. The Company may
      never achieve significant revenues or profitable operations.
 
    - ADDITIONAL FINANCING REQUIREMENTS. The Company's need for additional
      funding is expected to be substantial and will be determined by the
      progress and cost of the acquisition, development and commercialization of
      its products and other activities. Cash, cash equivalents and marketable
      securities on hand at September 30, 1998 will satisfy the Company's
      budgeted cash requirements for approximately 12 months. During that
      period, the Company will need to secure additional funding. If the Company
      experiences unanticipated cash requirements during that period, the
      Company could require funds much sooner. Failure to obtain adequate
      funding in a timely manner would have a material adverse effect on the
      Company's business, results of operations and cash flows.
 
    - EARLY STAGE OF DEVELOPMENT OF PROPRIETARY PRODUCTS; UNCERTAINTY OF FINAL
      PRODUCT DEVELOPMENT. While the Company's proposed proprietary products are
      in the development rather than the research stage, significant development
      remains prior to the time any of these proposed products may be brought to
      market. The Company's products currently under development may never be
      successfully developed, receive required governmental regulatory
      approvals, become commercially viable or achieve market acceptance.
 
    - MANUFACTURING RISK. The Company is manufacturing (through contract
      manufacturers and vendors) Nipent-Registered Trademark- and mitomycin, for
      sale. If, for any reason, the Company is unable to produce sufficient
      quantities of these products to satisfy market demand in a timely manner,
      the result could be a material adverse effect upon the Company's business,
      results of operations and cash flows. The Company also relies upon various
      domestic and foreign manufacturers and vendors for storage of crude
      concentrate, for production of certain of its bulk Extra and generic
      formulations and for production of sufficient quantities of compounds to
      conduct clinical trials for its proposed proprietary products. Failure of
      any of these manufacturers or vendors to successfully perform could have a
      material adverse effect upon the Company's business, results of operations
      and cash flows.
 
    - PHARMACEUTICAL DEVELOPMENT. The Company has obtained clearance from the
      FDA related to its Nipent-Registered Trademark- and mitomycin
      manufacturing processes and sources of bulk drugs for certain of its Extra
      and generic products. However, it has yet to receive marketing approval
      for any of its internally developed products, and such marketing approval
      may never be obtained.
 
    - DEPENDENCE ON KEY PERSONNEL. The Company's success is dependent on certain
      key management and scientific personnel, including Dr. Joseph Rubinfeld,
      the loss of whose services could significantly affect the ability of the
      Company to achieve its planned objectives. The loss of key personnel, or
      the inability to attract and retain the highly skilled personnel required
      to conduct and expand the Company's activities, could have a material
      adverse effect upon the Company's business, results of operations and cash
      flows.
 
    - NEED TO COMPLY WITH GOVERNMENTAL REGULATION AND TO OBTAIN PRODUCT
      APPROVALS. The Company cannot predict if or when it might submit its
      products currently under development for regulatory
 
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      review. Once the Company submits its potential products for review,
      regulatory approvals may never occur.
 
    - PATENTS AND PROPRIETARY TECHNOLOGY. The Company has licenses to or
      assignments of numerous issued U.S. patents but these may not provide any
      significant protection against competitors. Failure to comply with the
      terms of licenses and agreements could result in loss of the Company's
      underlying rights to one or more of its potential proprietary products.
      Claims against the Company may be raised based on patents held by others
      and such claims may be successful. If the Company becomes involved in any
      litigation, that process could consume a substantial portion of the
      Company's resources regardless of the outcome of such litigation.
 
    - COMPETITION. There are many companies, both public and private, including
      well-known pharmaceutical companies that are engaged in the development
      and sale of products for many of the applications being pursued by the
      Company. The industry in which the Company competes is characterized by
      extensive research and development efforts and rapid technological
      progress. Price erosion is also characteristic of this industry,
      particularly with regard to products such as the Company's proposed Extra
      and generic drugs. The Company's competitive position will be affected by
      many factors, including but not limited to:
 
        - the Company's ability to attract and retain qualified personnel,
          develop effective proprietary products, implement development and
          marketing plans, and secure adequate capital resources,
 
        - the ability of the Company to establish or maintain proprietary
          positions,
 
        - discoveries by others,
 
        - the number and success of competitors, and
 
        - market selling prices, inventory production costs and their effects
          upon the Company's gross margins.
 
    The above factors are not intended to be inclusive and there are numerous
other factors which could contribute to the business risk inherent in the
Company's operations. Some of these factors are described in the Company's
Annual Report on Form 10-K. Failure to satisfactorily achieve any of the
Company's objectives or avoid any of these risks may have a material adverse
effect on the Company's business, results of operations and cash flows.
 
IMPACT OF THE YEAR 2000 ISSUE
 
    The Year 2000 issue is the result of computer software applications being
written using two rather than four digits to define a year. On January 1, 2000,
computer equipment and programs that have time sensitive software may not be
able to distinguish whether "00" means 1900 or 2000. This could result in a
system failure or miscalculations causing disruptions of operations, including,
among other things, a temporary inability to process transactions, send
invoices, or engage in similar normal business activities.
 
    The Company converted to new accounting software in 1998 and that software
properly recognizes dates beyond December 31, 1999. The Company has determined
that no other software programs currently in use by the Company will require
significant modification or replacement to properly recognize dates beyond
December 31, 1999. The Company has initiated and maintains formal communications
with significant contract manufacturers, contract research organizations and
certain other vendors to determine the extent to which the Company is vulnerable
to those third parties' failure to remediate their own Year 2000 issues. Based
upon those communications, the Company believes that all significant computer
software programs utilized by third parties upon which the Company relies are
either Year 2000 compliant or will be converted to Year 2000 compliance prior to
December 31, 1999.
 
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    The total estimated cost of addressing and mitigating the Company's Year
2000 issue is less than $10,000.
 
    One or more of the Company's or its business partners' software applications
may prove to be non-Year 2000 compliant. In that case the Company may experience
difficulties on and after January 1, 2000. The worst case Year 2000 scenario
envisioned by the Company's management would involve delays in invoicing and
shipping, inventory production, and clinical trial documentation. The Company
believes that such delays, if encountered, would be addressed quickly and would
not result in a material adverse effect upon business, results of operations, or
cash.
 
    The Company is in the process of developing a contingency plan to address a
worst case Year 2000 scenario as described above and plans to complete this
contingency plan in the first quarter of 1999.
 
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                                   SIGNATURES
 
    Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.
 
Date:  January 14, 1999
 
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                                By:             /s/ JOSEPH RUBINFELD
                                      ----------------------------------------
                                              Joseph Rubinfeld, Ph.D.
                                      CHIEF EXECUTIVE OFFICER, PRESIDENT, AND
                                         DIRECTOR (PRINCIPAL EXECUTIVE AND
                                                 FINANCIAL OFFICER)
 
                                By:               /s/ KEVIN C. LEE
                                      ----------------------------------------
                                                    Kevin C. Lee
                                     CONTROLLER (PRINCIPAL ACCOUNTING OFFICER)
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